Biology subjects

Raynaud, C. M.

Publications and source records attributed to Raynaud, C. M..

4 recordsLinked to original sources

bioRxiv2026

Methylation-Guided Stratification of Colorectal Cancer Reveals Immune Subtypes with Distinct Clinical Outcomes

BackgroundAberrant DNA methylation is a hallmark of colorectal cancer (CRC). Yet, how DNA methylation is linked to transcriptional states, immune programs, and tissue resident microbiome within the same tumors has not been systematically analyzed. MethodsWe profiled genome-wide DNA methylation (Illumina MethylationEPIC) in 182 colon tumors and 76 adjacent normals from AC-ICAM, and integrated with matched transcriptomes, whole exome, microbiome, and clinical data. Tumor-specific methylation, promoter methylation-expression links, microbiome associations, and survival were analyzed and validated in TCGA-COAD. ResultsTumor and normal tissues exhibited distinct DNA methylation patterns, reflecting widespread epigenetic alterations in cancer. Pathway analysis identified two major tumor pathways regulated by DNA methylation. The first involved extracellular signaling and adhesion genes, with higher methylation linked to increased proliferation and lower immune infiltration. Similarly, higher tumor methylation in nitric oxide signaling was associated with reduced adaptive immune activity and interestingly, influenced immune-related survival. These findings were also validated in the TCGA-COAD cohort. An inverse methylation-expression pattern implicated modifications of TCR signaling in naive CD8, and interferon-/{beta} signaling which were hypermethylated and hypomethylated in tumors compared to normal, respectively. Combining methylation and microbiome revealed connections between Akkermansia muciniphila and TGF-{beta} and Prevotella nigrescens with MAPK signaling pathways. Finally, a methylation-based model using 43 promoters CpGs successfully identified patients with different survival outcomes, underscoring the clinical relevance of these epigenetic alterations in colon cancer. ConclusionDNA methylation shapes the molecular and immune landscape of colon cancer, altering signaling pathways and immune programs, interacting with the microbiome, and impacting patients survival.

cancer biology↗

bioRxiv2025

SLFN11 Enhances Cisplatin Sensitivity in Pediatric Cancer via Activation of Stress-Response and Suppression of Survival Pathways

Pediatric cancers pose significant treatment challenges due to their biological heterogeneity and variable responses to chemotherapy. SLFN11, a DNA/RNA helicase-like protein known to sensitize adult tumors to DNA-damaging agents, remains underexplored in pediatric malignancies. Here, we investigate the role of SLFN11 across pediatric Wilms tumor, osteosarcoma, and medulloblastoma using integrated bioinformatics, epigenetic profiling, and functional assays. In silico analysis of TARGET and ICGC datasets revealed distinct correlations between SLFN11 expression and patient survival, with positive, negative, or neutral predictive value depending on tumor type. Baseline expression and promoter methylation analysis in pediatric cancer cell lines demonstrated epigenetic regulation of SLFN11, similar to adult cancers. Using CRISPR-dCas9-mediated activation, we successfully upregulated SLFN11, which significantly enhanced sensitivity to cisplatin and the PARP inhibitor talazoparib across all tested cell lines. Transcriptomic profiling under cisplatin treatment indicated that SLFN11 modulates DNA damage response and MAPK signaling pathways, potentially contributing to chemotherapy sensitivity. These findings establish SLFN11 as a context-dependent predictive biomarker and a potential therapeutic target to overcome chemoresistance in pediatric solid cancers.

cancer biology↗

bioRxiv2024

MUC2 Expression Modulates Immune Infiltration in Colorectal Cancer

IntroductionColorectal cancer (CRC) is a prevalent malignancy with significant morbidity and mortality worldwide. A deeper understanding of the interaction of cancer cells with other cells in the tumor microenvironment is crucial for devising effective therapeutic strategies. MUC2, a major component of the protective mucus layer in the gastrointestinal tract, has been implicated in CRC progression and immune response regulation. MethodIn this study, we sought to elucidate the relationship between MUC2 expression and immune infiltration within CRC, using in-vitro models involving two well-established cell lines, HT-29 and LS-174T. By employing CRISPR-mediated MUC2 knockout, we investigated the influence of MUC2 on tumor immune infiltration and its interplay with T cells and NK cells enriched peripheral blood mononuclear cells (PBMCs) in 3D spheroid cultures. ResultsWhile MUC2 was more abundant in LS-174T cell lines compared to HT-29, its knockout resulted in increased immune infiltration solely in the HT-29 cell line, but not in LS-174T. We revealed that the removal of MUC2 protein was compensated in LS-174T by the expression of other gel forming mucin proteins (Muc6, Muc5B) commonly expressed in gastrointestinal epithelium, while this was not observed in HT-29 cell line. DiscussionWe propose that the role of MUC2 documented in CRC progression can partially be explained by impairing immune infiltration due to physical barrier established by the gel forming proteins such as MUC2 in mucinous CRC. On the other hand, the removal of MUC2 expression can be compensated by alternative gel forming mucin proteins, thereby impeding any increase in tumor immune infiltration.

cancer biology↗

bioRxiv2023

Modulation of SLFN11 induces changes in DNA Damage response

BackgroundLack of Schlafen family member 11 (SLFN11) expression has been recently identified as a dominant genomic determinant of response to DNA damaging agents in numerous cancer types. Thus, strategies aimed at increasing SLFN11 could be used to restore chemosensitivity of refractory cancers. As oncogenic downregulation is often driven by methylation of the promotor region, we explore the demethylation effect of 5-aza-2-deoxycytidine (decitabine), on the SLFN11 gene methylation. Since SLFN11 has been reported as an interferon inducible gene, and interferon is secreted during an active anti-tumor immune response, we investigated the in vitro effect of IFN-{gamma} on SLFN11 expression in breast cancer cell lines. A second broader approach to show cross talk between immune cells and SLFN11 expression is indirect co-culture of breast cancer cells with activated PBMCs and evaluate if this can drive SLFN11 upregulation. Finally, as a definitive and specific way to modulate SLFN11 expression we implemented SLFN11 dCas9 (dead CRISPR associated protein 9) systems to specifically increase or decrease SLFN11 expression. ResultsWe first confirmed a correlation previously reported between methylation of SLFN11 promoter and its expression across multiple cell lines. We showed in-vitro that decitabine and IFN-{gamma} could increase moderately the expression of SLFN11 in both BT- 549 and T47D cell lines, but not in strongly methylated cell lines such as MDA-MB-231. Though, in-vitro, the co-culture of the same cell lines with CD8-CD25 activated PBMC failed to increase SLFN11 expression. On the one hand, the use of a CRISPR-dCas9 UNISAM system could increase SLFN11 expression significantly (up to 5-fold), stably and specifically in BT-549 and T47D cancer cell lines. Though, this system also failed to force a strong expression of SLFN11 in cell lines with robust SLFN11 promoter methylation such as MDA-MB-231. On the other hand, the use of CRISPR-dCas9 KRAB could significantly reduce the expression of SLFN11 in BT-549 and T47D. We then used the modified cell lines to confirm the alteration in chemo sensitivity of those cells to treatment with DNA Damaging Agents (DDAs) such as Cisplatin and Epirubicin or DNA Damage Response (DDRs) drugs like Olaparib. RNAseq was used to elucidate the mechanisms of action affected by the alteration in SLFN11 expression. ConclusionTo our knowledge this is the first report of the stable non-lethal increase of SLFN11 expression in a cancer cell line. Our results show that induction of SLFN11 expression can enhance DDA and DDR sensitivity in breast cancer cells and dCas9 systems may represent a novel approach to increase SLFN11 and achieve higher sensitivity to chemotherapeutic agents, improving outcome or decreasing required drug concentrations. SLFN11-targeting therapies might be explored pre-clinically to develop personalized approaches.

cancer biology↗